Proteomics based diagnostic detection method for chronic sinusitis

ABSTRACT

The invention provides for a proteomic approach for identification of specific bacterial protein profiles that may be used in the development of methods for the diagnosis of bacterial chronic sinusitis. The invention provides for methods for determining the presence of pathogenic bacteria in the upper respiratory tract of a subject using protein profiles of the pathogenic bacteria. The invention also provides for methods of diagnosing a bacterial infection of the upper respiratory tract of a subject using protein profiles of a pathogenic bacteria. In addition, the invention provides for devices, immunoassays and kits for identifying pathogenic bacteria in the upper respiratory tract.

This application is a Continuation of U.S. Ser. No. 16/039,031 (now U.S.Pat. No. 10,345,300), filed Jul. 18, 2018, which is a Continuation ofU.S. Ser. No. 15/404,681, filed Jan. 12, 2017 (now U.S. Pat. No.10,048,261), which is a Divisional of U.S. patent application Ser. No.14/124,470, filed Jun. 16, 2014 (now U.S. Pat. No. 9,568,472), which isthe U.S. National Phase of International Application No.PCT/US2012/040910, filed Jun. 5, 2012, which claims priority benefit ofU.S. Provisional Patent Application No. 61/493,829, filed Jun. 6, 2011,which are incorporated by reference herein in their entirety.

This invention was made with government support under Grant Nos. R01DC05847 and KL2RR025754 awarded by the United States National Institutesof Health. The United States government has certain rights in theinvention.

FIELD OF INVENTION

The invention provides for a proteomic approach for identification ofspecific bacterial protein profiles that may be used in the developmentof methods for the diagnosis of bacterial chronic sinusitis. Theinvention provides for methods of determining the presence forpathogenic bacteria in the upper respiratory tract of a subject usingprotein profiles of the pathogenic bacteria. The invention also providesfor methods of diagnosing a bacterial infection of the upper respiratorytract of a subject using protein profiles of the pathogenic bacteria. Inaddition, the invention provides for devices, immunoassays and kits foridentifying pathogenic bacteria in the upper respiratory tract.

BACKGROUND

Otitis media, sinusitis, bronchitis, pharyngitis, and nonspecific upperrespiratory tract infections (URTI) account for approximately 75% ofoutpatient antibiotic prescriptions in the United States. Antibiotic useremains high despite the fact that greater than 85% of these infectionsare due to viruses and resolve without complication. Nonetheless, thoseremaining infections that are indeed due to bacterial pathogens requiremore effective management than is currently available. Bacterialcultures provide limited diagnostic value because the most commonbacteria responsible for URTI are also often commensal organisms in thenasopharynx.

Infections of the upper airway are the number one reason for officevisits in the US (American Academy of Pediatrics. Pediatrics, 2004.113:1451-1456. Center for Disease Control and Prevention web site,Gonzales R, et al. JAMA, 1997. 278(11):901-904, Nyquist A-C. JAMA, 1998.279(11): 875-877). About 52% of adults patients and 45% of pediatricpatients are prescribed antibiotics when diagnosed with an upper airwayinfection (Gonzales R, et al. JAMA, 1997. 278(11):901-904, Nyquist A-C.JAMA, 1998. 279(11): 875-877). Upper airway infections aremultifactorial and polymicrobial diseases. Infection by respiratoryviruses (e.g. RSV, adenovirus, rhinovirus, parainfluenza virus)predisposes to bacterial superinfection by members of the nasopharynxnormal flora: nontypeable Haemophilus influenzae, Streptococcuspneumoniae and Moraxella catarrhalis. While viral infections are oftenself-limiting, therapeutic delay of bacterial disease can lead tocomplications, permanent sequalae and severe morbidity and mortality.

Diagnosis is mainly based on clinical manifestations. Signs and symptomsof disease of bacterial and nonbacterial etiologies are oftenindistinguishable. Specific bacterial identification by traditionalmicrobiological culture techniques often fail to detect microorganismsgrowing within biofilms. Contamination of specimens by residentcolonizing flora often results in laboratory culture reports ofuncertain clinical value. Indiscriminate antibiotic use modifies thecommensal flora in the nasopharynx and induces the selection andemergence of microorganisms resistant to common antibiotics. Despite adecreasing trend in antibiotic prescription in recent years, unnecessaryand inappropriate antibiotic therapies are common, particularly in thetreatment of otitis media and sinusitis.

Upper respiratory tract infection remains as a major cause of overuse ofantibiotics and, therefore, a major contributor to the widespreademergence of antibiotic resistance. Therefore, there is a need for earlyand rapid diagnostic tests that could discriminate between commensal andpathogenic bacteria. These tests would promote judicious use ofantibiotic therapy, promote more effective choice of treatment andimprove outcomes.

SUMMARY OF INVENTION

Due to unique growth characteristics, bacterial biofilms produce adistinct set of proteins may be used to distinguish between commensaland pathogenic states. The invention provides for methods of identifyingthe protein profile of bacterial biofilms. The methodology involvesdetecting trace quantities of signature proteins that identify specificbacterial pathogens from typically sterile sites in the paranasal sinuscavities. As described herein, biofilms produced by nontypeableHaemophilus influenzae (NTHI) over 10 days generate a specific proteinprofile. Biofilms formed by NTHI in vitro release a signature set ofproteins into their environment that remains identifiable for severaldays. Outer membrane proteins (OMPs) are predominant components of theNTHI biofilm supernatant. Of particular interest are major OMPsassociated with bacterial virulence: outer membrane protein P5 (OMP P5)and outer membrane protein P2 (OMP P2). Additional OMPs include highmolecular weight adhesin 1/high molecular weight adhesin 2 (HMW1/HMW2),and IgA-protease. HMW1/HMW2, OMP P5 are mediators of adhesion toepithelial cells, OMP P2 is a porin and IgA protease functions to cleavehost IgA.

These studies support the development of a clinical diagnostic test anddevice for early and rapid identification of NTHI-associated URTIs,leading to a more effective choice of treatment and improved outcomes.NTHI was used as an example for the study but the same methods may beused to identify the presence of any pathogenic bacteria including thoseknown to cause chronic sinusitis such as Haemophiius influenza,Streptococcus pneumoniae, Moraxella catarrhalis, Staphylococcus aureus,Pseudomonas aeruginosa and Stenotrophomonas maltophilia.

The invention also provides for an immunoassay device that involvesobtaining a sample of the secretions within the typically sterileparanasal sinus cavities, and rapidly detecting the presence of tracequantities of signature proteins that identify specific bacterialpathogens from these typically sterile sites.

The invention provides for methods of detecting the presence of apathogenic bacteria in the upper respiratory tract of a subjectcomprising the steps of: a) obtaining a sample of secretions from theupper respiratory tract of the subject; b) generating a protein profileof the sample; c) comparing the protein profile with a reference proteinprofile, wherein the reference protein profile identifies a pathogenicbacteria; and d) determining whether the protein profile of the sampleassociates to the reference protein profile, wherein association isindicative of the presence of the pathogenic bacteria in the upperrespiratory tract of the subject.

The invention also provides for methods of detecting the presence of apathogenic bacteria in the upper respiratory tract of a subject asdescribed above wherein the method further comprises the step ofadministering a therapeutic compound to reduce or eliminate thepathogenic bacteria in the upper respiratory tract of the subject.Exemplary therapeutic compounds that reduce or eliminate pathogenicbacteria in the upper respiratory tract include antibiotics such aspenicillin, erythromycin, amoxicillin, thimethoprim-sulfamethoxazole,doxycyline, cefpodoxime, cefuroxime, cefdinir, clarithromycin,azithromycin, levofloxacin, gatifloxacin, and moxifloxacin,alpha-adreneric agonists such as oxymetazoline hydrochloride,anticholinergic (parasympatholytic) agents such as ipratropium bromide,antihistamines such as chlorpheniramine maleate, beta-agonistbronchodilators, non-steroidal anti-inflammatory drugs, camphor,menthol, Echinacea, mast cell stabilizers such as cromolyn sodium,topical nasal steroids such as fluticasone propionate and zinc salts.

The invention also provides for methods of detecting the presence of apathogenic bacteria in the upper respiratory tract of a subject asdescribed above wherein the method further comprises the step ofinforming the subject of the presence or absence of the pathogenicbacteria in the upper respiratory tract.

The invention also provides for methods of detecting the presence of apathogenic bacteria in the upper respiratory tract of a subject asdescribed above wherein the method further comprises the step ofdiagnosing the subject with a bacterial infection, wherein the presenceof the pathogenic bacteria in the upper respiratory tract of the subjectis indicative of a bacterial infection.

The term “pathogenic bacteria” refers to any disease causing bacteria.The term “commensal bacteria” refers to harmless or non-disease causingbacteria. The methods of the invention also may be used to distinguishthe presence of commensal bacteria verses pathogenic bacteria in theupper respiratory tract of a subject.

The invention also provides for methods of diagnosing a bacterialinfection in the upper respiratory tract of a subject comprising thesteps of: a) obtaining a sample of secretions from the upper respiratorytract of the subject; b) generating a protein profile of the sample; c)comparing the protein profile of the sample with a reference proteinprofile, wherein the reference protein profile identifies a pathogenicbacteria; and d) determining whether the protein profile of the sampleassociates to the protein profile; wherein association is indicative ofa bacterial infection in the upper respiratory tract of the subject.

The invention also provides for methods of diagnosing a bacterialinfection in the upper respiratory tract of a subject as described abovewherein the method further comprises the step of the step of informingthe subject of the diagnosis of a bacterial infection in the upperrespiratory tract.

The invention also provides for methods of diagnosing a bacterialinfection in the upper respiratory tract of a subject as described abovewherein the method further comprises the step of administering atherapeutic compound to treat the bacterial infection. A treatment for abacterial infection will reduce or alleviate the symptoms caused by thepathogenic bacteria or eliminate the bacteria from the site ofinfection. Exemplary therapeutic compounds that treat a bacterialinfection in the upper respiratory tract include antibiotics such aspenicillin, erythromycin, amoxicillin, thimethoprim-sulfamethoxazole,doxycyline, cefpodoxime, cefuroxime, cefdinir, clarithromycin,azithromycin, levofloxacin, gatifloxacin, and moxifloxacin,alpha-adreneric agonists such as oxymetazoline hydrochloride,anticholinergic (parasympatholytic) agents such as ipratropium bromide,antihistamines such as chlorpheniramine maleate, beta-agonistbronchodilators, non-steroidal anti-inflammatory drugs, camphor,menthol, Echinacea, mast cell stabilizers such as cromolyn sodium,topical nasal steroids such as fluticasone propionate, budenoside,mometasone, triamcinolone, and dexamethasone, and zinc salts. The term“protein profile” refers to at least one protein that is at leastpartially identified or characterized so that the presence or absence ofthe protein in any particular sample may be monitored. The term“reference protein profile” refers to a protein profile generated for aknown control or standard sample.

A protein profile of a sample associates with a reference proteinprofile when one or more the proteins in the reference profile arepresent in the sample profile at a concentration that indicatesinfection or pathogenicity of the bacteria. To determine if a sampleprotein profile associates with a reference protein profile, theprofiles are scored to predict how likely the mass of a fragment that itdetected is likely from the peptide sequence it is predicted it to be,and how much quantity of the peptide there is in the supernatant.Software programs that analyze mass spectrometry data may be used. Forexample, Mascot (Matrix Science, Boston, Mass.), performs massspectrometry data analysis through a statistical evaluation of matchesbetween observed and projected peptide fragments rather than crosscorrelation may be used to determine in the sample associates with areference protein profile. See, e.g., D. N. Perkins, et al.,Electrophoresis, 20(18) 3551-67 (1999).

The preceding methods may be carried out for any pathogenic bacteriawhich infects the upper respiratory tract, including Haemophilusinfluenzae, Streptococcus pneumoniae, Moraxella catarrhalis,Staphylococcus aureus, Pseudomonas aeruginosa or Stenotrophomonasmaltophilia.

The invention also provides for uses of a therapeutic compound for thepreparation of a medicament to reduce or eliminate the pathogenicbacteria in the upper respiratory tract of a subject or uses to treat abacterial infection in the upper respiratory tract of a subject, whereinthe subject has a protein profile that associates to a reference proteinprofile, and wherein the association is indicative of the presence ofthe pathogenic bacteria or bacterial infection in the upper respiratorytract of the subject as determined by any of the preceding methods ofdetecting the presence of a pathogenic bacteria or diagnosing abacterial infection in the upper respiratory tract of a subject.

The invention also provides for therapeutic compositions for thereduction or elimination of a pathogenic bacteria in the upperrespiratory tract of a subject or for the treatment of a bacterialinfection in the upper respiratory tract of a subject, wherein thesubject has a protein profile that associates to a reference proteinprofile, and wherein the association is indicative of the presence ofthe pathogenic bacteria or bacterial infection in the upper respiratorytract of the subject tract of the subject as determined by any of thepreceding methods of detecting the presence of a pathogenic bacteria ordiagnosing a bacterial infection in the upper respiratory tract of asubject.

Exemplary therapeutic compounds that treat a bacterial infection in theupper respiratory tract include antibiotics such as penicillin,erythromycin, amoxicillin, thimethoprim-sulfamethoxazole, doxycyline,cefpodoxime, cefuroxime, cefdinir, clarithromycin, azithromycin,levofloxacin, gatifloxacin, and moxifloxacin, alpha-adreneric agonistssuch as oxymetazoline hydrochloride, anticholinergic (parasympatholytic)agents such as ipratropium bromide, antihistamines such aschlorpheniramine maleate, beta-agonist bronchodilators, non-steroidalanti-inflammatory drugs, camphor, menthol, Echinacea, mast cellstabilizers such as cromolyn sodium, topical nasal steroids such asfluticasone propionate, budenoside, mometasone, triamcinolone, anddexamethasone, and zinc salts.

In another aspect of the invention, the invention provides for methodsof detecting the presence of nontypeable Haemophilus influenzae (NTHI)bacteria in the upper respiratory tract of a subject comprising thesteps of: a) obtaining a sample from the upper respiratory tract of thesubject; b) detecting the presence of at least one biomarker in thesample, wherein the biomarkers are selected from the group consistingof: HMW1/HMW2, OMP P5, OMP P2 and IgA-protease, and wherein the presenceof at least one biomarker indicates the presence of NTHI bacteria in theupper respiratory tract of the subject. In one embodiment, the methodcomprises detecting the presence of OMP P2 and/or OMP P5 in the sample,wherein the presence of OMP P2 and/or OMP P5 indicates the presence ofNTHI bacteria in the upper respiratory tract of the subject.

The invention also provides for methods of detecting the presence ofNTHI bacteria in the upper respiratory tract of a subject wherein themethod further comprises the step of administering a therapeuticcompound to reduce or eliminate the NTHI bacteria in the upperrespiratory tract of the subject. Exemplary therapeutic compounds thatreduce or eliminate the NTHI bacteria in the upper respiratory tractinclude antibiotics such as penicillin, erythromycin, amoxicillin,thimethoprim-sulfamethoxazole, doxycyline, cefpodoxime, cefuroxime,cefdinir, clarithromycin, azithromycin, levofloxacin, gatifloxacin, andmoxifloxacin, alpha-adreneric agonists such as oxymetazolinehydrochloride, anticholinergic (parasympatholytic) agents such asipratropium bromide, antihistamines such as chlorpheniramine maleate,beta-agonist bronchodilators, non-steroidal anti-inflammatory drugs,camphor, menthol, Echinacea, mast cell stabilizers such as cromolynsodium, topical nasal steroids such as fluticasone propionate,budenoside, mometasone, triamcinolone, and dexamethasone, and zincsalts.

The invention also provides for methods of diagnosing a NTHI infectionin the upper respiratory tract of a subject comprising the steps of: a)obtaining a sample of secretions from the upper respiratory tract of thesubject, b) detecting the presence of at least one biomarker in thesample, wherein the biomarkers are selected from the group consistingof: HMW1/HMW2. OMP P5, OMP P2 and IgA-protease, and wherein the presenceof at least one biomarkers indicates an NTHI infection in the upperrespiratory tract of the subject. In one embodiment, the methodcomprises detecting the presence of OMP P2 and/or OMP P5 in the sample,wherein the presence of OMP P2 and/or OMP P5 indicates a NTHI bacterialinfection in the upper respiratory tract of the subject.

The invention also provides for methods of diagnosing a NTHI infectionin the upper respiratory tract of a subject as described above whereinthe method further comprises the step of informing the subject of thediagnosis of a NTHI infection in the upper respiratory tract.

The invention also provides for methods of diagnosing NTHI infection inthe upper respiratory tract of a subject as described above wherein themethod further comprises the step of administering a therapeuticcompound to treat the NTHI infection in the upper respiratory tract ofthe subject. A treatment for a NTHI infection will reduce or alleviatethe symptoms caused by the NTHI bacteria or eliminate the NTHI bacteriafrom the site of infection. Exemplary therapeutic compounds that treat aNTHI infection in the upper respiratory tract include antibiotics suchas penicillin, erythromycin, amoxicillin, thimethoprim-sulfamethoxazole,doxycyline, cefpodoxime, cefuroxime, cefdinir, clarithromycin,azithromycin, levofloxacin, gatifloxacin, and moxifloxacin,alpha-adreneric agonists such as oxymetazoline hydrochloride,anticholinergic (parasympatholytic) agents such as ipratropium bromide,antihistamines such as chlorpheniramine maleate, beta-agonistbronchodilators, non-steroidal anti-inflammatory drugs, camphor,menthol, Echinacea, mast cell stabilizers such as cromolyn sodium,topical nasal steroids such as fluticasone propionate, budenoside,mometasone, triamcinolone, and dexamethasone, and zinc salts.

The term “upper respiratory tract” includes the nose or nostrils, nasalcavity, mouth, throat (pharynx), paranasal sinus cavity and voice box(larynx). The respiratory system is lined with a mucous membrane thatsecretes mucus or fluid. This secreted mucus and fluid is referred toherein as “secretions.” In any of the preceding methods, the sample ofsecretions may be collected from the paranasal sinus cavity includingthe middle meatus or the ethmoid infundibulum. The “paranasal sinuscavity” refers to the frontal sinuses (in the forehead), maxillarysinuses (behind the cheek bones), ethmoid sinuses (between the eyes) andthe sphenoid sinuses (behind the eyes).

The invention also provides for use of a therapeutic compound for thepreparation of a medicament to reduce or eliminate NTHI bacteria in theupper respiratory tract of a subject or to treat a NTHi infection in theupper respiratory tract of a subject, wherein the presence of NTHIbacteria or a NTHI infection is determined by the presence of at leastone biomarker selected from OMP P2 and OMP P5 as determined by any ofthe preceding methods of detecting the presence of a NTHI bacterial ordiagnosing a NTHI infection in the upper respiratory tract of a subjectmethod as determined by the preceding methods of detecting the presenceof NTHI bacteria or diagnosing a NTHI infection in the upper respiratorytract of a subject.

The invention also provides for a therapeutic composition for thereduction or elimination of NTHI bacteria or for the treatment of NTHIinfection in the upper respiratory tract of a subject, wherein thepresence of NTHi bacteria or NTHI infection as determined by any of thepreceding methods of detecting the presence of a NTHI bacterial ordiagnosing a NTHI infection in the upper respiratory tract of a subject.

Any of the preceding methods, uses or therapeutic compositions may becarried out on a subject suffering from chronic sinusitis, or a subjectthat is prone to suffering from recurrent acute sinusitis. In addition,any of the preceding methods may be carried out on a subject sufferingfrom Otitis media, bronchitis, pharyngitis, and nonspecific upperrespiratory tract infections.

The invention also provides for methods, uses or therapeuticcompositions for treating chronic sinusitis or a pathogenic bacterialinfection of the upper respiratory tract in a subject comprisingdetecting a pathogenic bacteria in the upper respiratory tract of thesubject using any of the preceding methods and administering theappropriate dose of a therapeutic compound known to effectively treatthe particular pathogenic bacteria detected within the upper respiratorytract of the subject. A treatment for a chronic sinusitis or apathogenic bacterial infection will reduce or alleviate the symptomscaused by the pathogenic bacteria or eliminate the pathogenic bacteriafrom the site of the infection. Exemplary therapeutic compounds includeantibiotics such as penicillin, erythromycin, amoxicillin,thimethoprim-sulfamethoxazole, doxycyline, cefpodoxime, cefuroxime,cefdinir, clarithromycin, azithromycin, levofloxacin, gatifloxacin, andmoxifloxacin, alpha-adreneric agonists such as oxymetazolinehydrochloride, anticholinergic (parasympatholytic) agents such asipratropium bromide, antihistamines such as chlorpheniramine maleate,beta-agonist bronchodilators, non-steroidal anti-inflammatory drugs,camphor, menthol, Echinacea, mast cell stabilizers such as cromolynsodium, topical nasal steroids such as fluticasone propionate,budenoside, mometasone, triamcinolone, and dexamethasone, and zincsalts.

The invention also provides for methods of treating, uses andtherapeutic compositions for chronic sinusitis or a pathogenic bacterialinfection of the upper respiratory tract in a subject comprisingdiagnosing a pathogenic bacteria infection in the upper respiratorytract of the subject using any of the preceding methods andadministering the appropriate dose of a therapeutic compound known toeffectively treat the particular pathogenic bacteria detected within theupper respiratory tract of the subject. Exemplary therapeutic compoundsinclude antibiotics such as penicillin, erythromycin, amoxicillin,thimethoprim-sulfamethoxazole, doxycyline, cefpodoxime, cefuroxime,cefdinir, clarithromycin, azithromycin, levofloxacin, gatifloxacin, andmoxifloxacin, alpha-adreneric agonists such as oxymetazolinehydrochloride, anticholinergic (parasympatholytic) agents such asipratropium bromide, antihistamines such as chlorpheniramine maleate,beta-agonist bronchodilators, non-steroidal anti-inflammatory drugs,camphor, menthol, Echinacea, mast cell stabilizers such as cromolynsodium, topical nasal steroids such as fluticasone propionate,budenoside, mometasone, triamcinolone, and dexamethasone and zinc salts.

In any of the preceding methods, uses or therapeutic compositions of theinvention, the sample may be collected using sterile swabs, sterilegauze, nasal washing, suction tube or a balloon catheter.

For the detecting step in any of the preceding methods of the invention,the biomarker may be detected using a monoclonal antibody. In addition,an immunoassay may be used to detect the biomarker of interest in any ofthe preceding methods of the invention.

In any of the preceding methods of the invention, the sample may becollected with a device comprising a substrate presenting antibodiesspecific for the biomarkers of interest, such as a balloon catheterwherein the substrate is threaded into the suction port of the catheter.

An another aspect of the invention provides for immunoassays fordetecting the presence of a pathogenic bacteria in the upper respiratorytract of a subject comprising the steps of a) obtaining a sample ofsecretions from the upper respiratory tract of the subject using adevice comprising antibodies specific for at least one biomarkerassociated with the presence of a pathogenic bacteria in the upperrespiratory tract of the subject; b) detecting the presence of at leastone biomarker associated with the presence of a pathogenic bacteria inthe upper respiratory tract of the subject to generate a proteinprofile; c) comparing the protein profile with a reference proteinprofile, wherein the reference protein profile identifies a pathogenicbacteria; and d) determining whether the protein profile of the sampleassociates to the reference protein profile, wherein association isindicative of the presence of the pathogenic bacteria in the upperrespiratory tract of the subject.

The term “immunoassay” is a laboratory approach to directly orindirectly detect protein or peptide in fluid, e.g. biological fluid, byuse of an immunological reaction between an antigen and an antibody.

The term “antibody” is synonymous with “immunoglobulin,” and includesnaturally occurring human antibodies, polyclonal antibodies, andmonoclonal antibodies. The term “antibody” is meant to include both thenative antibody and biologically active and synthetic derivatives ofantibodies, such as, for example, Fab′, F(ab″)₂ or Fv as well assingle-domain and single-chain antibodies. A biologically activederivative of an antibody retains the ability to bind an antigen. Inparticular, the invention provides for methods and immunoassays that useantibodies specific for the biomarkers of interests, such as monoclonalantibodies that specifically bind biomarkers of interest, e.g. OMP P2and OMP P5.

In addition, the immunoassays described above may further comprising astep of diagnosing the subject with a bacterial infection wherein thepresence of the pathogenic bacteria in the upper respiratory tract ofthe subject is indicative of a bacterial infection.

The invention also provides for any of the preceding immunoassay furthercomprising the step of administering a therapeutic compound in an amounteffective to treat the bacterial infection. Exemplary therapeuticcompounds include antibiotics such as penicillin, erythromycin,amoxicillin, thimethoprim-sulfamethoxazole, doxycyline, cefpodoxime,cefuroxime, cefdinir, clarithromycin, azithromycin, levofloxacin,gatifloxacin, and moxifloxacin, alpha-adreneric agonists such asoxymetazoline hydrochloride, anticholinergic (parasympatholytic) agentssuch as ipratropium bromide, antihistamines such as chlorpheniraminemaleate, beta-agonist bronchodilators, non-steroidal anti-inflammatorydrugs, camphor, menthol, Echinacea, mast cell stabilizers such ascromolyn sodium, topical nasal steroids such as fluticasone propionate,budenoside, mometasone, triamcinolone, and dexamethasone, and zincsalts.

In any of the preceding immunoassays, the pathogenic bacteria detectedmay be Haemophilus influenzae, Streptococcus pneumoniae, Moraxellacatarrhalis, Staphylococcus aureus, Pseudomonas aeruginosa orStenotrophomonas maltophilia.

The invention also provides for uses of a therapeutic compound for thepreparation of a medicament to reduce or eliminate NTHI bacteria in theupper respiratory tract of a subject or to treat a NTHi infection in theupper respiratory tract of a subject, wherein the presence of NTHibacterial or a NTHi infection is determined by the presence of at leastone biomarker selected from OMP P2 and OMP P5 as determined by any ofthe preceding

In addition, the invention provides for a therapeutic composition forthe reduction or elimination of NTHI bacteria in the upper respiratorytract of a subject or for the treatment of NTHI infection in the upperairway of a subject, wherein the presence of NTHi bacteria or NTHIinfection is determined by the presence of at least one biomarkerselected from OMP P2 and OMP P5 as determined by any of the precedingimmunoassays.

In another aspect of the invention, the invention provides forimmunoassays for detecting the presence of a nontypeable NTHI bacteriain the upper respiratory tract of a subject comprising the steps of a)obtaining a sample of secretions from the upper respiratory tract of thesubject using a device comprising antibodies specific for at least onebiomarker associated with the presence of a NTHI bacteria in the upperrespiratory tract of the subject, wherein at least one biomarker is OMPP2 or OMP P5; b) detecting the presence of at least one biomarkerassociated with the presence of a NTHI bacteria in the upper respiratorytract of the subject to generate a protein profile; c) comparing theprotein profile with a reference protein profile, wherein the referenceprotein profile identifies NTHI bacteria; and d) determining whether theprotein profile of the sample associates to the reference proteinprofile, wherein association is indicative of the presence of the NTHIbacteria in the upper respiratory tract of the subject.

The invention also provides for immunoassays for detecting the presenceNTHI bacteria in the upper respiratory tract of a subject as describedabove further comprising a step of diagnosing the subject with a NTHIinfection wherein the presence of NTHI bacteria in the upper respiratorytract of the subject is indicative of a NTHI infection.

The invention also provides for any of the preceding immunoassays, whichfurther comprise the step of administering a therapeutic compound in anamount effective to treat the bacterial infection. Exemplary therapeuticcompounds include antibiotics such as penicillin, erythromycin,amoxicillin, thimethoprim-sulfamethoxazole, doxycyline, cefpodoxime,cefuroxime, cefdinir, clarithromycin, azithromycin, levofloxacin,gatifloxacin, and moxifloxacin, alpha-adreneric agonists such asoxymetazoline hydrochloride, anticholinergic (parasympatholytic) agentssuch as ipratropium bromide, antihistamines such as chlorpheniraminemaleate, beta-agonist bronchodilators, non-steroidal anti-inflammatorydrugs, camphor, menthol, Echinacea, mast cell stabilizers such ascromolyn sodium, topical nasal steroids such as fluticasone propionate,budenoside, mometasone, triamcinolone, and dexamethasone, and zincsalts.

In another aspect of the invention, the invention provides forimmunoassays for diagnosing a NTHI infection in the upper respiratorytract of a subject comprising the steps of a) obtaining a sample ofsecretions from the upper respiratory tract of the subject using adevice comprising antibodies specific for at least one biomarkerassociated with the presence of a NTHI in the upper respiratory tract ofthe subject, wherein the at least one biomarker is OMP P2 or OMP P5; b)detecting the presence of at least one biomarker associated with thepresence of a NTHI in the upper respiratory tract of the subject togenerate a protein profile; c) comparing the protein profile with areference protein profile, wherein the reference protein profileidentifies NTHI; and d) determining whether the protein profile of thesample associates to the reference protein profile, wherein associationis indicative of a NTHI infection in the upper respiratory tract of thesubject.

The invention also provides for any of the preceding immunoassaysfurther comprising the step of informing the subject of the presence ofa NTHI bacteria or a NTHI infection in the upper respiratory tract ofthe subject. Exemplary therapeutic compounds include antibiotics such aspenicillin, erythromycin, amoxicillin, thimethoprim-sulfamethoxazole,doxycyline, cefpodoxime, cefuroxime, cefdinir, clarithromycin,azithromycin, levofloxacin, gatifloxacin, and moxifloxacin,alpha-adreneric agonists such as oxymetazoline hydrochloride,anticholinergic (parasympatholytic) agents such as ipratropium bromide,antihistamines such as chlorpheniramine maleate, beta-agonistbronchodilators, non-steroidal anti-inflammatory drugs, camphor,menthol, Echinacea, mast cell stabilizers such as cromolyn sodium,topical nasal steroids such as fluticasone propionate, budenoside,mometasone, triamcinolone, and dexamethasone, and zinc salts.

In addition, the sample used in any of the preceding immunoassays may beobtained using a sterile swab, sterile gauze, suction tube or a ballooncatheter.

In another aspect of the invention, the invention provides for a devicefor obtaining a sample of secretions from the upper respiratory tract ofa subject comprising a substrate presenting antibodies specific for atleast one biomarker associated with the presence of a pathogenicbacteria in the upper respiratory tract of the subject.

The invention also provides for devices for carrying out any of thepreceding methods of the invention or any of the preceding immunoassaysof the invention which is used for obtaining a sample of secretions fromthe upper respiratory tract of a subject comprising a substratepresenting antibodies specific for biomarkers associated with thepresence of a pathogenic bacteria in the upper respiratory tract of thesubject.

In any of the preceding devices, the antibodies may be specific for OMPP2 or OMP P5, such as monoclonal antibodies that specifically bind NTHIOMP P2 or monoclonal antibodies that specifically bind NTHI OMP P5.

In another aspect of the invention, the invention provides for kits forcarrying out any of the preceding methods or immunoassays. In oneembodiment, the kits comprise a substrate presenting antibodies specificfor at least one biomarker associated with the presence of a pathogenicbacteria or a bacterial infection in the upper respiratory tract of thesubject. In another embodiment, the kits comprise devices for obtainingthe sample from the sterile compartments within the upper respiratorytract of the subject and generating a protein profile associated with apathogenic bacteria or bacterial infection in the upper respiratorytract of the subject. The kits may also comprise antibodies thatspecifically bind the protein biomarkers of interest and components forimmunoassays to detect the protein biomarkers using these antibodies.

BRIEF DESCRIPTION OF DRAWINGS

FIG. 1 depicts a silver stain of the distinct protein profile maintainedover time in the NTHI biofilm supernatant.

FIG. 2 depicts a Western blot analysis verifying the presence of theNTHI OMPs in NTHI biofilm supernatant.

FIG. 3 depicts a Western blot analysis verifying the presence of OMP P2and OMP P5 in the biofilm supernatant of various strains of NTHI.

DETAILED DESCRIPTION

The invention provides for methods with improved sensitivity andspecificity for detecting and diagnosing bacterial sinusitis. Inparticular, the methods of invention comprise antibody-based bacterialdetection of proteins within secretions of pathogenic biofilm locatedwithin the paranasal sinus cavities. These methods allow for thedetection of trace quantities of signature proteins that identifyspecific bacterial pathogens from typically sterile sites in theparanasal sinus cavities. The methods of the invention provide for theability to avoid broad-spectrum, empiric antibiotics which are ofteninappropriately given treat upper viral respiratory infections due tothe difficulty in diagnosing bacterial sinusitis with a high sensitivityand high specificity. The methods of the invention are an improvementover typical bacterial cultures because these cultures have very lowsensitivity for detecting bacterial biofilms and low specificity fordistinguishing between commensal and pathogenic organisms.

The invention also provides for a device that involves delivering a wirethrough a balloon catheter to the typically sterile paranasal sinuscavities, sampling mucus from these sites, and rapidly detecting thepresence of trace quantities of signature proteins that identifyspecific bacterial pathogens from these typically sterile sites. Uponobtaining the sample, an immunoassay may be run to generate a proteinprofile that is compared to a reference protein profile generated forthe pathogenic bacteria known to cause chronic sinusitis or an infectionof the upper respiratory tract.

Biomarkers

The term “biomarker” refers to a naturally occurring molecule, gene, orcharacteristic by which a particular pathological or physiologicalprocess, disease, or the like can be identified or characterized. Theterm “biomarker” may refer to a protein measured in sample whoseconcentration reflects the severity or presence of some disease state.Biomarkers may be measured to identify risk for, diagnosis of orprogression of a pathological or physiological process, disease or thelike. Exemplary biomarkers include proteins, hormones, prohormones,lipids, carbohydrates, DNA, RNA and combinations thereof.

For example, biomarkers for NTHI pathogenic bacteria include outermembrane protein P2 (OMP P2: SEQ ID NO: 1), high molecular weightadhesin 1 (HMW1A; SEQ ID NO: 2), putative periplasmic chelated ironbinding proteins (SEQ ID NO: 3), IgA-specific serine endopeptidase (SEQID NO: 4), outer membrane protein P5 (OMP P5; SEQ ID NO: 5),galactose-1-phosphate uridylyltransferase (SEQ ID NO: 6), HMWA (SEQ IDNO: 7), phosphate ABC transporter phosphate-binding protein (SEQ ID NO:8), putative adhesin B precursor FimA (SEQ ID NO: 9), high molecularweight adhesin 2 (HMW2A; SEQ ID NO: 10), outer membrane protein P5precursor (SEQ ID NO: 11) and outer membrane protein P1 (OMP P1; SEQ IDNO: 12).

The methods of the invention include detecting at least one biomarker,at least two biomarkers, at least three biomarkers, at least fourbiomarkers, at least five biomarkers or six or more biomarkers of theprotein profile of a pathogenic bacteria. Detection of the proteinbiomarkers includes detecting full length or fragments of the proteinbiomarkers, including immunogenic or biologically active fragments. Inparticular, the methods of the invention include detecting at least OMPP2 and OMP 5 to generate a protein profile of NTHI bacteria.

The invention also provides biologically active or immunologicallyactive variants of the amino acid sequences of the present invention;and “substantial equivalents” thereof (e.g., with at least about 65%, atleast about 70%, at least about 75%, at least about 80%, at least about85%, 86%, 87%, 88%, 89%, at least about 90%, 91%, 92%, 93%, 94%,typically at least about 95%, 96%, 97%, more typically at least about98%, or most typically at least about 99% amino acid identity) thatretain biological and/or immunogenic activity. Polypeptides encoded byallelic variants may have a similar, increased, or decreased activitycompared to polypeptides encoded by the native polynucleotides.

The present invention further provides isolated polypeptides or peptidesencoded by the nucleic acid fragments or by degenerate variants of thenucleic acid fragments. The term “degenerate variant” refers tonucleotide fragments which differ from a native nucleic acid fragment(e.g., an ORF) by nucleotide sequence but, due to the degeneracy of thegenetic code, encode an identical polypeptide sequence. Preferrednucleic acid fragments are the ORFs that encode proteins.

The invention also provides for polypeptides with one or moreconservative amino acid substitutions that do not affect the biologicaland/or immunogenic activity of the polypeptide. Alternatively, thepolypeptides are contemplated to have conservative amino acidssubstitutions which may or may not alter biological activity. The term“conservative amino acid substitution” refers to a substitution of anative amino acid residue with a nonnative residue, including naturallyoccurring and nonnaturally occurring amino acids, such that there islittle or no effect on the polarity or charge of the amino acid residueat that position. For example, a conservative substitution results fromthe replacement of a non-polar residue in a polypeptide with any othernon-polar residue. Further, any native residue in the polypeptide mayalso be substituted with alanine, according to the methods of “alaninescanning mutagenesis”. Naturally occurring amino acids are characterizedbased on their side chains as follows: basic: arginine, lysine,histidine; acidic: glutamic acid, aspartic acid; uncharged polar:glutamine, asparagine, serine, threonine, tyrosine; and non-polar:phenylalanine, tryptophan, cysteine, glycine, alanine, valine, proline,methionine, leucine, norleucine, isoleucine. General rules for aminoacid substitutions are set forth in Table 1 below.

TABLE 1 Amino Acid Substitutions Original Residues ExemplarySubstitutions Preferred Substitutions Ala Val, Leu, Ile Val Arg Lys,Gln, Asn Lys Asn Gln Gln Asp Glu Glu Cys Ser, Ala Ser Gln Asn Asn GluAsp Asn Gly Pro, Ala Ala His Asn, Gln, Lys, Arg Arg Ile Leu, Val, Met,Ala, Phe, Leu Leu Norleucine, Ile, Val, Met, Leu Lys Arg, 1,4Diaminobutyric Arg Met Leu, Phe, Ile Leu Phe Leu, Val, Ile, Ala, Tyr ArgPro Ala Gly Ser Thr, Ala, Cys Thr Thr Ser Ser Trp Tyr, Phe Tyr Tyr Trp,Phe, Thr, Ser Phe Val Ile, Met, Leu, Phe, Ala, Leu

The polypeptides may be encoded by nucleotide sequences that aresubstantially equivalent to the polynucleotides encoding the polypeptidebiomarkers. Polynucleotides according to the invention can have, e.g.,at least 65%, at least 70%, at least 75%, at least 80%, 81%, 82%, 83%,84%, 85%, 86%, 87%, 88%, or 89%, more typically at least 90%, 91%, 92%,93%, or 94% and even more typically at least 95%, 96%, 97%, 98% or 99%sequence identity to the native polynucleotide sequences.

Included within the scope of the nucleic acid sequences of the inventionare nucleic acid sequence fragments that hybridize under stringentconditions to the nucleotide sequences encoding the polypeptidebiomarkers or compliments thereof, which fragment is greater than about5 nucleotides, preferably 7 nucleotides, more preferably greater than 9nucleotides and most preferably greater than 17 nucleotides. Fragmentsof, e.g., 15, 17, or 20 nucleotides or more that are selective for(i.e., specifically hybridize to any one of the polynucleotides of theinvention) are contemplated. Probes capable of specifically hybridizingto a polynucleotide can differentiate polynucleotide sequences of theinvention from other polynucleotide sequences in the same family ofgenes or can differentiate genes from other bacterial genes, and arepreferably based on unique nucleotide sequences.

The term “stringent” is used to refer to conditions that are commonlyunderstood in the art as stringent. Hybridization stringency isprincipally determined by temperature, ionic strength, and theconcentration of denaturing agents such as formamide. Examples ofstringent conditions for hybridization and washing are 0.015 M sodiumchloride, 0.0015M sodium citrate at 65-68° C. or 0.015 M sodiumchloride, 0.0015M sodium citrate, and 50% formamide at 42° C. SeeSambrook et al., Molecular Cloning: A Laboratory Manual, 2.sup.nd Ed.,Cold Spring Harbor Laboratory, (Cold Spring Harbor, N.Y. 1989). Morestringent conditions (such as higher temperature, lower ionic strength,higher formamide, or other denaturing agent) may also be used, however,the rate of hybridization will be affected. In instances whereinhybridization of deoxyoligonucleotides is concerned, additionalexemplary stringent hybridization conditions include washing in 6×.SSC0.05% sodium pyrophosphate at 37° C. (for 14-base oligos), 48° C. (for17-base oligos), 55° C. (for 20-base oligos), and 60° C. (for 23-baseoligos).

Other agents may be included in the hybridization and washing buffersfor the purpose of reducing non-specific and/or backgroundhybridization. Examples are 0.1% bovine serum albumin, 0.1%polyvinyl-pyrrolidone, 0.1% sodium pyrophosphate, 0.1% sodium dodecylsulfate, NaDodSO₄, (SDS), ficoll, Denhardt's solution, sonicated salmonsperm DNA (or other non-complementary DNA), and dextran sulfate,although other suitable agents can also be used. The concentration andtypes of these additives can be changed without substantially affectingthe stringency of the hybridization conditions. Hybridizationexperiments are usually carried out at pH 6.8-7.4, however, at typicalionic strength conditions, the rate of hybridization is nearlyindependent of pH. See Anderson et al., Nucleic Acid Hybridisation: APractical Approach, Ch. 4, IRL Press Limited (Oxford, England; 1985).Hybridization conditions can be adjusted by one skilled in the art inorder to accommodate these variables and allow DNAs of differentsequence relatedness to form hybrids.

The sequences falling within the scope of the present invention are notlimited to these specific sequences, but also include allelic andspecies variations thereof. Preferred computer program methods todetermine identity and similarity between two sequences include, but arenot limited to, the GCG program package, including GAP (Devereux et al.,Nucl. Acid. Res., 12:387, -1984; Genetics Computer Group, University ofWisconsin, Madison, Wis.), BLASTP, BLASTN, and FASTA (Altschul et al.,J. Mol. Biol., 215: 403-410, 1990). The BLASTX program is publiclyavailable from the National Center for Biotechnology Information (NCBI)and other sources (BLAST Manual, Altschul et al. NCB/NILM/NIH Bethesda,Md. 20894; Altschul et al., supra). The well known Smith Watermanalgorithm may also be used to determine identity.

Methods of Generating Protein Profiles

The methods of the invention involve generating a protein profile ofsecretion samples obtained from the upper respiratory tract of a subjectand generating protein profiles of pathogenic bacteria biofilmsupernatants. The known pathogenic bacteria biofilm protein profiles maybe used as reference protein profiles for use in the methods of theinvention.

Separation of protein of interest from the other members of the proteinprofile may be accomplished by any number of techniques, such as sucrosegradient centrifugation, aqueous or organic partitioning (e.g.,two-phase partitioning), non-denaturing gel electrophoresis, isoelectricfocusing gel electrophoresis, capillary electrophoresis,isotachyphoresis, mass spectroscopy, chromatography (e.g., HPLC),polyacrylamide gel electrophoresis (PAGE, such as SDS-PAGE), gelpermeation, ion-exchange spin columns, and the like. In theseembodiments, SELDI, or other rapid analysis techniques, may be used formonitoring the purification process. Following purification, allpotential biomarkers may be characterized by SDS PAGE and massspectrometry and identified by peptide mapping and/or amino acidsequence analysis.

For example, the protein biomarkers may be separated by size or buoyantdensity gradient separation method, such as a discontinuous sucrosegradient, that separates the component polypeptides of the sample by thesizes of the complexes in which they participate. Sucrose gradients forthe separation of proteins are well known, and may be modified asneeded. Such modifications may include the use of a continuous, ratherthan discontinuous gradient, and different gradient conditions (forinstance, different sucrose concentrations or different buffers). Thelength of the gradient can also be varied, with longer gradientsexpected to give better overall separation of proteins and proteincomplexes, and to provide a larger number of fractions that are theneach individually analyzed using a denaturing system.

The individual protein biomarkers may be separated by electrophoresisbased upon size (e.g., by SDS-PAGE or sizing gel). Other separationtechniques may include aqueous two-phase partitioning and non-denaturingagarose gel electrophoresis separation. In other embodiments, separationemploys denaturing system such as an isoelectric focusing (IEF) gel,capillary electrophoresis, or isotachyphoresis. Alternatively oradditionally, two-dimensional electrophoretic analysis may be used(e.g., Wilkins et al., Proteome Research: New Frontiers in FunctionalGenomics, Springer-Verlag, Berlin, 1997). Proteins can be visualized onsuch gels using any of various stains known in the art (e.g., TrypanBlue or SyproRuby dye). Traditional buffering systems can also be usedfor separating proteins in the component fractionations of the describedsystems. The temperature, voltage, and amperage at which individual gelsare run also can be modified, as can the speed and duration of gradientequilibration and centrifugation.

Purification of protein biomarkers be performed using traditionalchromatographic techniques. In an embodiment, high pressure liquidchromatography (HPLC) may be used. Also, a combination of high pressureliquid chromatography (HPLC) and sodium dodecyl sulfate polyacrylamidegel electrophoresis (SDS-PAGE) may be used to purify the protein. Thefractions may then be assayed for the protein of interest using SELDI orother methods.

A variety of methods may be used to generate the protein profile such ascertain Matrix Assisted Laser Desorption Ionization (MALDI) MassSpectrometry technology, Surface Enhanced Laser Desorption/Ionization(SELDI) and Protein Chip Mass Spectrometry.

The methods may include steps for analyzing the protein profile. In anembodiment, analysis of the protein profile comprises a statisticalanalysis and other data manipulation techniques (e.g., signalprocessing, removal of noise). In some embodiments, techniques foranalysis comprise computer statistical and data processing software. Forexample, analysis of the protein profile may comprise a determination ofat least one of the molecular weight (mass), net charge, and or amountof the proteins in the sample.

The method may also comprise the step of comparing the protein profilefor the subject's sample to a reference protein profile. In addition tobiofilm protein profiles generated for known strains of bacteria, thereference profile may be from a healthy control subject who does notexhibit symptoms of the disease of interest (i.e., a negative control).The reference profile may be from a subject who has a disease ofinterest (i.e., a positive control). Also, the sample protein profilemay be compared to a reference protein profile isolated from the samesubject, but at a different point in time (e.g., to monitor progressionor remission of the disease). In yet other embodiments, the sampleprotein profile may be compared to a plurality of a reference proteinprofiles, as for example, reference profiles generated as diagnostic ofa particular disease or disease subtype. In this way, it may be possibleto determine whether the sample protein profile matches a particularprotein or proteins of interest that are typical of any one disease ordisease subtype.

Kits and Devices for Carrying Out the Methods of the Invention

The invention provides for kits for carrying out the methods andimmunoassays of the invention. In one embodiment, the kits comprisedevices for obtaining the secretion sample from the sterile compartmentswithin the upper respiratory tract of the subject. The kits may alsocomprise antibodies that specifically bind the protein biomarkers ofinterest and components for immunoassays to detect the proteinbiomarkers using these antibodies. In addition, the kits may comprisesubstrates presenting antibodies specific for the protein biomarkers ofinterest. Furthermore, the kits may comprise instructions for carryingout the any of the methods or immunoassays of the invention.

In one embodiment, secretions from the upper respiratory tract may beobtained using sterile swabs or gauze. In another embodiment of theinvention, the secretion sample may be collected using nasal washingmethods. Alternatively, the secretion sample may be collected using asuction tube attached to an electric pump and a catheter inserted intothe nasopharynx of the subject.

In another embodiment, the device for obtaining the secretion sample isa modified balloon catheter Seldinger technique that allows forcollection of secretions from the sterile compartments within the upperrespiratory tract of the subject. The balloon catheter may have asubstrate presenting antibodies specific for the protein biomarkers ofinterest threaded into the catheter. In a further embodiment, a modifieddistal chip brochoesophagoscope or transnasal esophagoscope may be usedin which a substrate presenting antibodies specific for the proteinbiomarkers of interest is threaded into the suction port of the device.

The invention provides for an immunoassay for detecting at least onebiomarker that is specific for a biofilm protein profile for apathogenic bacteria. For example, antibodies specific for two or morebiomarkers within the protein profile are presented or absorbed to asolid substrate, and the secretion sample obtained from the upper airwayof the respiratory tract of a subject are contacted with the solidsubstrate and binding of the antibody to the substrate is detected.

Any type of immunoassay system known in the art may be used to detectthe biomarkers of the protein profiles. Exemplary methods include, butnot limited to: radioimmunoassays, ELISA assays, sandwich assays,precipitin reactions, gel diffusion precipitin reactions,immunodiffusion assays, agglutination assays, fluorescent immunoassays,protein A immunoassays and immunoelectrophoresis assays and any othermethods of generating a protein profile described herein. Theimmunoassays may be a sandwich assay in which the target analyte(biomarker of interest) is “sandwiched” between a labeled antibody andan antibody immobilized on the solid substrate. The immunoassay is readby observing the presence and amount of antigen-labeled antibody complexbound to the immobilized antibody. Another immunoassay may also be a“competition” type immunoassay, wherein an antibody immobilized on asolid surface is contacted with a sample (e.g., secretions from theupper respiratory tract) containing both an unknown quantity of antigenanalyte (biomarker of interest) and with labeled antigen of the sametype. The amount of labeled antigen bound on the solid substrate is thendetermined to provide an indirect measure of the amount of antigenanalyte (biomarker of interest) in the sample. Such immunoassays arereadily performed in a “dipstick” or other test device format (e.g., aflow-through or migratory dipstick or other test device design) forconvenient use. For example, numerous types of dipstick immunoassaysassays are described in U.S. Pat. No. 5,656,448.

The immune assays may be carried out on sheets, e.g. strips or sheets ofnitrocellulose or polyvinylidene difloride (PVDH) or other membranes,dipstick, wells e.g. 96-well plastic plates, or in tubes.

A device used in the methods and immunoassays of the invention can, forexample, provide a color indication when the biomarker of interest iswithin the secretion sample from the upper respiratory tract of asubject. The device could be used in a clinical setting to quicklydetermine if a subject has a pathological bacteria or a bacterialinfection in the upper respiratory tract. Alternatively, the methods andimmunoassays of the present invention may be used in combination with adensitometer or generally a device for measuring light intensity,transmittance, reflection or refraction, or for measuring the wavelengthof light as a measure of assay result. The densitometer or other devicecan provide rapid measurement of the optical density of the substratewithin the device that have been contacted with the secretions sample.In one embodiment, a change in color, density, or other parameter can beread by the naked eye.

The invention also may be carried out using a lateral-flow immunoassaywhich contains a device within the assay to extract the sample foranalysis, and antibodies specific for the proteins within the proteinprofile of a pathogenic bacteria of interest. The invention alsoprovides for a immunoassay device, for example, such as those describedin U.S. Pat. Nos. 5,415,994 and 5,763,262, which comprise a proteinprofile identified for a particular pathogenic bacteria using any of themethod of the invention. In particular, the invention provides forcolorimetric immunoassays that allow for visual detection of thebiomarkers of interest within the secretion sample. Visual detectionallows for a rapid result which can be incorporated into a treatmentplan for the infection.

A reference or standard protein profile may be used in the methods ofthe invention to compare the sample protein profile generated by themethods, immunoassays or kits of the invention. The reference orstandard protein profile provides the concentration of a biomarker knownto be present in the biofilm secretion of a pathogenic bacteria withinthe upper respiratory tract during an infection. A “calibrator” refersto immunoassays that detect known amounts of biomarkers of interest togenerate a calibration curve to quantify the concentration of thebiomarker in an unknown biological fluid.

The term “standard” or “reference” refers to immunoassays that measurebiomarkers of interest from biological fluids known to be collected froma subject having a bacterial infection of the upper respiratory tract ina suitable quantitative form to control the quality of reagentscontained in an immunoassay kit of the present invention. Other aspectsand advantages of the present invention will be understood uponconsideration of the following illustrative examples.

EXAMPLES Example 1 Determination of Signature Protein Profile forPathogenic Bacteria

Supernatants from nontypeable H. influenzae (NTHI) biofilm were analyzedto determine the NTHI signature protein profile. NTHI strain 86-028NPwas cultured in eight-well chamber slides for 10 days and the resultingsupernatants were collected at 24 hours intervals. The proteins in thesupernatants collected from NTHI biofilm cultures were separated bySDS-PAGE and silver stain revealed a distinct protein profile maintainedover time as shown in FIG. 1.

The proteins isolated from NTHI biofilm supernatants were analyzed bynano-liquid chromatography/tandem mass spectrometry (LC-MS/MS). Themolecular weights of the identified proteins were compared to themolecular weights of the known protein profile for the NTHI strain86-028NP ((Bakaletz et al. Infection and Immunity, 56(2): 331-335,1988), and the identified proteins were scored based on theirassociation to the 86-028NP protein profile using Mascot (MatrixScience, Boston Mass.) according to the manufacturer's instructions. Theresults of this comparison are set out in Table 2 below. Several NTHIouter membrane proteins (OMPs) were identified (in bold), withpredominance of major OMPs (bold italics): high molecular weightadhesins 1 and 2 (HMW1/HMW2), OMP P5, OMP P2, OMP P1, and IgA-protease.

In order to verify the presence of the NTHI OMPs in NTHI biofilmsupernatants, Western blot analysis was carried out with antiserumagainst total OMPs, OMP P5 and OMP P2 (chinchilla polyclonalantibodies), as well as HMW1 and HMW2 proteins (monoclonal antibodies).This analysis verified the presence of multiple NTHI-specific OMPs inbiofilm supernatants (see FIG. 2).

TABLE 2 SEQ Mass ID IDENTIFIED PROTEIN Score (kDa) Accession # NO:

1227 39.9 gi|68248747 1

, high molecular weight 1205 154.5 gi|68250281 2 adhesin 1 putativeperiplasmic chelated iron 1089 32.4 gi|301169065 3 binding protein

 

948 197.5 gi|68249575 4 Outer membrane

886 38.4 gi|68249712 5 galactose-1-phosphate 791 34.0 gi|145640927 6uridylyltransferase

720 160.5 gi|68249817 7 phosphate ABC transporter 703 36.6 gi|16273649 8phosphate-binding protein putative adhesin B precursor FimA 402 35.0gi|3003012 9 HMW2A, high molecular weight 326 160.7 gi|68249817 10adhesin 2 HMWA 321 160.5 gi|5929966 11 Outer membrane protein P5; 28337.7 gi|585614 12 Precursor Outer membrane

215 49.7 gi|9716607 13

One example of a signature protein profile of pathogenic NTHI biofilm isOMP P5, OMP P2, HMW1 and HMW2. Therefore, detection of these proteinbiomarkers in a secretion sample obtained from the upper respiratorytract is indicative of NTHI infection. Precise diagnosis of pathogenicbacterial infection, such as NTHI infection, in patients with upperairway infection will facilitate the selection of appropriate therapyand promote judicious prescription of antibiotics in order to achieve anearly recovery in patients and to reduce the emergence ofantibiotic-resistant infections in the community.

Example 2 Detection of NTHI Biofilm-Specific Proteins in Paranasal SinusInfection

In order to determine the protein profile of a human patient sufferingfrom sinusitis, secretion samples are obtained from the upperrespiratory tract of the patients. These samples are analyzed asdescribed in Example 1 for the presence of OMP P5, OMP P2, HMW1 andHMW2. The protein profile of the patients is compared with the referenceprotein profile generated from the supernatants of in vitro NTHIbiofilms as described above.

Example 3 Identification of Protein Biomarkers Associated with OtherBacteria Species

The methods described in Example 1 are carried out with the supernatantsfrom biofilms of other pathogenic bacteria species such as Streptococcuspneumonia, Moraxella catarrhalis, Staphylococcus aureus, Pseudomonasaeruginosa and Stenotrophomonas maltophilia.

Example 4 Further Analysis of Determination of Signature Protein Profilefor Pathogenic Bacteria

Supernatants from biofilm obtained from multiple stains of nontypeableH. influenzae (NTHI) were analyzed to define the NTHI signature proteinprofile. NTHI strains 86-028NP, 1128MEE, 1714, 1748, 1885MEE and 2019were cultured in eight-well chamber slides for 10 days and the resultingsupernatants were collected at 24 hours intervals. The proteins in thesupernatants collected from NTHI biofilm cultures were separated bySDS-PAGE and silver staining revealed a distinct protein profilemaintained over time. FIG. 3 depicts a Western blot using chinchillaanti-OMP P2 or anti-OMP P5 antibodies, which demonstrates that OMP P2and OMP P5 are present in high levels in the biofilms of all NTHIstrains tested.

The proteins isolated from NTHI biofilm supernatants were analyzed bynano-liquid chromatography/tandem mass spectrometry (LC-MS/MS). Themolecular weights of the identified proteins were compared to themolecular weights of the known protein profile for the NTHI strain86-028NP ((Bakaletz et al. Infection and Immunity, 56(2): 331-335,1988), and the identified proteins were scored based on theirassociation to the 86-028NP protein profile using Mascot (MatrixScience, Boston Mass.) according to the manufacturer's instructions. Theresults of this comparison are set out in Table 3 below. These studiesdemonstrate that a preferred NTHI biofilm protein profile comprises OMPP2 and OMP P5.

TABLE 3 Score Description Organism P2 Fragment 2927 Outer membraneprotein P2 H. influenzae 771 Outer membrane protein P5 H. influenzae 688Spermidine/putrescine-binding periplasmic H. influenzae protein 1 352Keratin, type II cytoskeletal 2 epidermal Homo sapiens 335 Trypsin Susscrofa 292 Protein mrp homolog H. influenzae 165 3-dehydroquinatesynthase H. influenzae 143 Phenylalanyl-tRNA synthetase alpha chain H.influenzae 105 Glutamate 5-kinase H. influenzae 100Aspartate-semialdehyde dehydrogenase H. influenzae P5 Fragment 1512Lipoprotein E H. influenzae 1105 Outer membrane protein P2 H. influenzae718 Hybrid peroxiredoxin hyPrx5 H. influenzae 361 Outer membrane proteinP5 H. influenzae 354 Trypsin OS = Sus scrofa Sus scrofa 2552,3,4,5-tetrahydropyridine-2,6-dicarboxylate N- H. influenzaesuccinyltransferase 168 Putative glutamine amidotransferase HI_1037 H.influenzae 167 Phosphate import ATP-binding protein PstB H. influenzae124 Dihydrodipicolinate reductase H. influenzae 118 Ig kappa chain Cregion M. musculus

The isolated proteins were also purified using cationic and gelchromatography. The purified OMP P2 and OMP P5 protein will be used togenerate monoclonal antibodies for use in the methods, immunoassays anddevices of the invention. It is critical that the antibodies used in themethods, immunoassays and devices of the invention be highly specific.The currently available chinchilla polyclonal antibodies do not exhibitthe specificity necessary for carrying out the methods of the invention.

Example 5 Generation of Monoclonal Antibodies

The purified OMP P2 and OMP P5 proteins described in Example 4 are usedto generate monoclonal antibodies for use in the methods, immunoassaysand devices of the invention using standard techniques well known in theart.

For example, a mouse is immunized intraperitoneally with the purifiedOMP P2 protein or purified OMP P5 protein. Four days later, the mouse issacrificed and spleen cells are fused with murine myeloma cells usingmethods standard in the art. For example, hybridoma technology isdescribed in Kohler et al., Nature 256: 495-7 (1975), the human B-cellhybridoma technique is described in Kozbor et al., Immunol. Today 4, 72(1983), the EBV-hybridoma technique to produce human monoclonalantibodies is described in Cole et al. Monoclonal Antibodies in CancerTherapy (1985) Allen R. Bliss, Inc., pages 77-96, and methods ofscreening combinatorial antibody libraries is described in Huse et al.,Science 246, 1275 (1989).

The fused cells are cloned in a 96-well plate for single colonyselection. Seven to ten days after fusion, culture supernatants fromeach well with colonies are assayed for the presence of anti-OMP P2 oranti-OMP P5 antibodies. Two to four weeks after cloning, supernatantsfrom single cell colonies are screen for the presence of anti-OMP P2 oranti-OMP P5 antibodies again. Wells with positive reactions are furtherexpanded into larger wells and eventually expanded into flasks toharvest more supernatant for further testing.

Hybridoma cells from the positive clones are injected into pristine micefor production of ascites. The monoclonal antibodies are purified fromthe ascites, and the specificity of the purified monoclonal antibodiesis tested using standard assays known in the art.

Example 6 Immunoassays of the Invention

Anti-OMP P2 and OPM P5 monoclonal antibodies, as described in Example 5,are used to determine the protein profile of a human patient sufferingfrom sinusitis. Secretion samples are obtained from the upperrespiratory tract of the patients. These samples are analyzed asdescribed in Example 1 for the presence of at least OMP P5, OMP P2, HMW1or HMW2. The protein profile of the patients is compared with thereference protein profile generated from the supernatants of in vitroNTHI biofilms as described above

The sensitivity and specificity parameters for the use of anti-OMP P2and anti-OPM P5 monoclonal antibodies, as described in Example 5, aredetermined against a gold-standard real-time PCR assay using hpd as aprimer for the detection of nontypeable Haemophilus influenzae that hasbeen shown to be 100% specific and sensitive for the detection of NTHIstrains 86-028NP, 1128MEE, 1714, 1748, 1885MEE and 2019 and severalclinical isolates of Moraxella catarrhalis.

Numerous modifications and variations in the practice of the inventionare expected to occur to those of skill in the art upon consideration ofthe presently preferred embodiments thereof. Consequently, the onlylimitation which should be placed upon the scope of the invention arethose which appear in the appended claims.

What is claimed:
 1. A method of detecting the presence of a pathologicalbacteria in an upper respiratory tract of a subject, the methodcomprising: contacting at least a portion of a sample of secretions fromthe upper respiratory tract of the subject with a flow-through or amigratory dipstick assay device; detecting the presence of-an outermembrane protein (OMP) from the pathological bacteria by contacting thesample with antibodies specific for the OMP, wherein the pathologicalbacteria is nontypeable Haemophilus influenzae (NTHI), Streptococcuspneumoniae, Moraxella catarrhalis, Staphylococcus aureus, Pseudomonasaeruginosa, or Stenotrophomonas maltophilia.
 2. The method of claim 1,wherein the flow-through or a migratory dipstick assay device comprisesa substrate onto which antibodies specific for the outer membraneprotein (OMP) have been immobilized.
 3. The method of claim 1, furthercomprising inserting a collection device into the patient's respiratorytract to obtain the sample of secretions from the respiratory tract ofthe subject.
 4. The method of claim 3, wherein inserting the collectiondevice into the patient's upper respiratory tract comprises inserting aswab.
 5. The method of claim 1, further comprising administering atherapeutic compound to the subject to reduce or eliminate the NTHIbacteria in the upper respiratory tract of the subject to treat one ormore of: Otitis media, bronchitis, or pharyngitis.
 6. The method ofclaim 1, wherein the OMP is selected from the group consisting of: highmolecular weight adhesin 1 (HMW1), high molecular weight adhesin 2(HMW2), outer membrane protein 5 (OMP P5), outer membrane protein P2(OMP P2), IgA-protease, putative periplasmic chelated iron bindingproteins, IgA-specific serine endopeptidase, galactose-1-phosphateuridylyltransferase, HMWA, phosphate ABC transporter phosphate-bindingprotein, putative adhesin B precursor FimA, and outer membrane proteinP1 (OMP P1).
 7. The method of claim 1, wherein the OMP comprises highmolecular weight adhesin 1 (HMW1).
 8. The method of claim 1, wherein theOMP comprises high molecular weight adhesin 2 (HMW2).
 9. The method ofclaim 1, wherein the OMP comprises IgA-protease.
 10. A method ofdetecting the presence of a pathological bacteria in an upperrespiratory tract of a subject, the method comprising: contacting asample of secretions from the upper respiratory tract of the subjectwith a substrate onto which antibodies specific for an outer membraneprotein (OMP) from the pathological bacteria; and detecting theantibodies specific for an OMP, wherein the pathological bacteria isnontypeable Haemophilus influenzae (NTHI) Streptococcus pneumoniae,Moraxella catarrhalis, Staphylococcus aureus, Pseudomonas aeruginosa, orStenotrophomonas maltophilia.
 11. The method of claim 10, furthercomprising inserting a collection device into the patient's upperrespiratory tract to obtain the sample of secretions from therespiratory tract of the subject.
 12. The method of claim 11, whereininserting the collection device into the patient's upper respiratorytract comprises inserting a swab.
 13. The method of claim 10, whereincontacting the sample comprises contacting the sample with aflow-through or migratory dipstick assay device including the substrate.14. The method of claim 10, further comprising administering atherapeutic compound to the subject to reduce or eliminate the NTHIbacteria in the upper respiratory tract of the subject to treat one ormore of: Otitis media, bronchitis, or pharyngitis.
 15. The method ofclaim 10, wherein the OMP is selected from the group consisting of: highmolecular weight adhesin 1 (HMW1), high molecular weight adhesin 2(HMW2), outer membrane protein 5 (OMP P5), outer membrane protein P2(OMP P2), IgA-protease, putative periplasmic chelated iron bindingproteins, IgA-specific serine endopeptidase, galactose-1-phosphateuridylyltransferase, HMWA, phosphate ABC transporter phosphate-bindingprotein, putative adhesin B precursor FimA, and outer membrane proteinP1 (OMP P1).
 16. The method of claim 10, wherein the OMP comprises highmolecular weight adhesin 1 (HMW1).
 17. The method of claim 10, whereinthe OMP comprises high molecular weight adhesin 2 (HMW2).
 18. The methodof claim 10, wherein the OMP comprises IgA-protease.
 19. A method ofdetecting the presence of a pathological bacteria in an upperrespiratory tract of a subject, the method comprising: contacting asample of secretions from the upper respiratory tract of the subjectwith a substrate onto which antibodies specific for an outer membraneprotein (OMP) from the pathological bacteria; contacting the sample withlabeled antibodies specific for the at least one biomarker associatedwith the presence of a pathological bacteria; and detecting the labeledantibody, wherein the pathological bacteria is nontypeable Haemophilusinfluenzae (NTHI), Streptococcus pneumoniae, Moraxella catarrhalis,Staphylococcus aureus, Pseudomonas aeruginosa, or Stenotrophomonasmaltophilia.